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comparison carboseqSimulator.xml @ 1:8e2dd4aec727 draft

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author siwaa
date Tue, 25 Jun 2024 10:36:43 +0000
parents df440714e49a
children bf6c51b72a10
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0:df440714e49a 1:8e2dd4aec727
1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.0"> 1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.1">
2 <description>To run the CarboSeq simulator</description> 2 <description>To run the CarboSeq simulator</description>
3 <requirements> 3 <requirements>
4 <container type="singularity">docker://registry.forgemia.inra.fr/carboseq/csopralibs_dev:paralleltoparallelly</container> 4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:develop-695457e0</container>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 bash -e -c "mkdir inputs && 7 bash -e -c "mkdir inputs &&
8 mkdir output &&
8 unzip -d input ${input} && 9 unzip -d input ${input} &&
9 set -a ;source /usr/local/src/myscripts/.env && 10 set -a ;source /usr/local/src/myscripts/.env &&
10 export CARBOSEQPREPROCESSOR_INPUT_DIR=\$(realpath -s input) 11 Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r --url=https://coby.infosol.inrae.fr:7777/semantify --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --NBCores=\${GALAXY_SLOTS:-4}&&
11 export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) && 12 mv output/* ${output}"
12 Rscript /usr/local/src/myscripts/scenarios/run-sim-perf/run.r &&
13 cd output &&
14 zip -r output.zip * &&
15 cp output.zip ${output}"
16 ]]> 13 ]]>
17 </command> 14 </command>
18 <inputs> 15 <inputs>
19 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/> 16 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
20 </inputs> 17 </inputs>
21 <outputs> 18 <outputs>
22 <data format='zip' name="output" label="CarboSeq output (zip)"/> 19 <data format='rdata' name="output" label="CarboSeq output (rdata)"/>
23 </outputs> 20 </outputs>
24 <tests> 21 <tests>
25 </tests> 22 </tests>
26 <help> 23 <help>
27 the CarboSeq CarboseqSimulator tool 24 the CarboSeq CarboseqSimulator tool